This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Core 2 seeks to improve proteome analyses through a multitude of technological advancements. These advancements have been achieved by extending the capabilities to include non-conventional nanogram-sized and smaller samples, by enhancing the dynamic range of the MS measurements, by applying new methods of analyzing intact proteins, by high sensitivity phosphoproteome profiling, by advancements in sample processing, by improving stable isotope labeling with oxygen-18 and its extension to LC-SRM measurements, by high resolution FAIMS development, through the application of iTRAQ quantification, by developing a multiplexed quantification strategy for phosphopeptides, by improving biofluid proteome coverage, by making additional advances in MS sensitivity, and by high throughput 2D nano-LC-MS. A description of NCRR supplements that facilitate the paradigm shift to population proteomics is provided.